Comparative Analysis of Intergenic Regions

A comparison of A. mexicanum V-V intergenic length was made with D. rerio (GRCz11) and H. sapiens (GRCh38.p12). In these cases, coordinate data was obtained from ENSEMBL gff dump (54 (link)). As for X. tropicalis, we performed a new X. tropicalis IGH locus annotation based on the corresponding ENSEMBL annotation (Xenopus_tropicalis_v9.1, GCA_000004195.3), further complemented and refined with sequence data kindly provided by Sibayshi Das (2 (link)), and X. tropicalis liver RNA-seq data (SRR579561) (55 (link)) following the same methodology as for A. mexicanum.

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Martinez-Barnetche J., Godoy-Lozano E.E., Saint Remy-Hernández S., Pacheco-Olvera D.L., Téllez-Sosa J., Valdovinos-Torres H., Pastelin-Palacios R., Mena H., Zambrano L, & López-Macías C. (2023). Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum. Frontiers in Immunology, 14, 1039274.

Publication 2023

Dump Igh locus Liver Rna seq Xenopus

Corresponding Organization : Hospital de Especialidades

Other organizations : Instituto Politécnico Nacional, Universidad Nacional Autónoma de México

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Variable analysis

independent variables

A. mexicanum
D. rerio
H. sapiens
X. tropicalis

dependent variables

V-V intergenic length

control variables

Coordinate data obtained from ENSEMBL gff dump (54 (link))
X. tropicalis IGH locus annotation based on the corresponding ENSEMBL annotation (Xenopus_tropicalis_v9.1, GCA_000004195.3), further complemented and refined with sequence data kindly provided by Sibayshi Das (2 (link)), and X. tropicalis liver RNA-seq data (SRR579561) (55 (link)) following the same methodology as for A. mexicanum

Annotations

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